[2024-01-24 13:37:28,230] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:28,232] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:28,232] [INFO] DQC Reference Directory: /var/lib/cwl/stg76d45e4f-817f-4619-9eb1-5f1b977ed49f/dqc_reference
[2024-01-24 13:37:29,494] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:29,495] [INFO] Task started: Prodigal
[2024-01-24 13:37:29,495] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2bc434f-75a5-4ad4-8515-de099718e0c5/GCF_014196135.1_ASM1419613v1_genomic.fna.gz | prodigal -d GCF_014196135.1_ASM1419613v1_genomic.fna/cds.fna -a GCF_014196135.1_ASM1419613v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:39,996] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:39,997] [INFO] Task started: HMMsearch
[2024-01-24 13:37:39,997] [INFO] Running command: hmmsearch --tblout GCF_014196135.1_ASM1419613v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76d45e4f-817f-4619-9eb1-5f1b977ed49f/dqc_reference/reference_markers.hmm GCF_014196135.1_ASM1419613v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:40,270] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:40,271] [INFO] Found 6/6 markers.
[2024-01-24 13:37:40,307] [INFO] Query marker FASTA was written to GCF_014196135.1_ASM1419613v1_genomic.fna/markers.fasta
[2024-01-24 13:37:40,307] [INFO] Task started: Blastn
[2024-01-24 13:37:40,307] [INFO] Running command: blastn -query GCF_014196135.1_ASM1419613v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76d45e4f-817f-4619-9eb1-5f1b977ed49f/dqc_reference/reference_markers.fasta -out GCF_014196135.1_ASM1419613v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:41,339] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:41,344] [INFO] Selected 21 target genomes.
[2024-01-24 13:37:41,344] [INFO] Target genome list was writen to GCF_014196135.1_ASM1419613v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:41,472] [INFO] Task started: fastANI
[2024-01-24 13:37:41,473] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2bc434f-75a5-4ad4-8515-de099718e0c5/GCF_014196135.1_ASM1419613v1_genomic.fna.gz --refList GCF_014196135.1_ASM1419613v1_genomic.fna/target_genomes.txt --output GCF_014196135.1_ASM1419613v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:58,401] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:58,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76d45e4f-817f-4619-9eb1-5f1b977ed49f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:58,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76d45e4f-817f-4619-9eb1-5f1b977ed49f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:58,422] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:58,422] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:58,423] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	100.0	1198	1199	95	conclusive
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	99.9949	1198	1199	95	conclusive
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	80.5017	568	1199	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	80.2695	548	1199	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	80.1934	420	1199	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	80.1146	566	1199	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	80.112	562	1199	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	80.0891	562	1199	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.0562	576	1199	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	80.0043	530	1199	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.9878	519	1199	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.9431	546	1199	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	79.8729	577	1199	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	79.8469	454	1199	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.76	569	1199	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	79.5922	507	1199	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	79.5439	500	1199	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.5105	460	1199	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	78.7376	401	1199	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	78.6353	357	1199	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	77.8861	276	1199	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:58,424] [INFO] DFAST Taxonomy check result was written to GCF_014196135.1_ASM1419613v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:58,428] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:58,428] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:58,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76d45e4f-817f-4619-9eb1-5f1b977ed49f/dqc_reference/checkm_data
[2024-01-24 13:37:58,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:58,471] [INFO] Task started: CheckM
[2024-01-24 13:37:58,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196135.1_ASM1419613v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196135.1_ASM1419613v1_genomic.fna/checkm_input GCF_014196135.1_ASM1419613v1_genomic.fna/checkm_result
[2024-01-24 13:38:32,905] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:32,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:32,926] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:32,927] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:32,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196135.1_ASM1419613v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:32,928] [INFO] Task started: Blastn
[2024-01-24 13:38:32,928] [INFO] Running command: blastn -query GCF_014196135.1_ASM1419613v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76d45e4f-817f-4619-9eb1-5f1b977ed49f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196135.1_ASM1419613v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:34,875] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:34,878] [INFO] Selected 19 target genomes.
[2024-01-24 13:38:34,878] [INFO] Target genome list was writen to GCF_014196135.1_ASM1419613v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:34,965] [INFO] Task started: fastANI
[2024-01-24 13:38:34,965] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2bc434f-75a5-4ad4-8515-de099718e0c5/GCF_014196135.1_ASM1419613v1_genomic.fna.gz --refList GCF_014196135.1_ASM1419613v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196135.1_ASM1419613v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:49,721] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:49,737] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:49,737] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_004135605.1	s__Sphingomonas desiccabilis	99.9949	1198	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004341505.2	s__Sphingomonas sp004341505	91.8685	968	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCA_017744835.1	s__Sphingomonas sp017744835	80.7106	544	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096895.1	s__Sphingomonas sp003096895	80.3152	543	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761945.1	s__Sphingomonas leidyi	80.2549	549	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.87	98.83	0.90	0.87	3	-
GCF_001619955.1	s__Sphingomonas hankookensis	80.1055	541	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.49	99.35	0.90	0.87	3	-
GCA_003240755.1	s__Sphingomonas hengshuiensis_A	80.0608	503	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127225.1	s__Sphingomonas sp002127225	80.0444	554	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421765.1	s__Sphingomonas sp001421765	80.0309	539	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014641735.1	s__Sphingomonas metalli	79.9943	518	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345855.1	s__Sphingomonas sp004345855	79.9108	596	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421355.1	s__Sphingomonas sp001421355	79.88	540	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.29	96.58	0.97	0.94	3	-
GCF_001555965.1	s__Sphingomonas sp001555965	79.7788	450	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCF_014334115.1	s__Sphingomonas sp014334115	79.7747	467	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421715.1	s__Sphingomonas sp001421715	79.6182	538	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.52	97.51	0.91	0.91	3	-
GCF_003515075.1	s__Sphingomonas gilva	79.5762	508	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792685.1	s__Sphingomonas gei	79.5703	496	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550065.1	s__Sphingomonas caeni	79.3105	449	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003171655.1	s__Sphingomonas portus	78.7482	400	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:49,739] [INFO] GTDB search result was written to GCF_014196135.1_ASM1419613v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:49,740] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:49,745] [INFO] DFAST_QC result json was written to GCF_014196135.1_ASM1419613v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:49,745] [INFO] DFAST_QC completed!
[2024-01-24 13:38:49,745] [INFO] Total running time: 0h1m22s